Historically, 3d models were created with non-standard scale, origin or orientation and this was corrected for in the footprint definition. However it was decided to standardise the footprint and 3d models, so that they have the same standard parameters. Because 3d models and footprints are in different files, they became out of step. People who get the footprints via github plugin find that the footprints are updated but not the 3d models.
Therefore, if you can use the latest 3d models and the latest footprints they should be in sync.